1. Bioinformatics Lecture 2

2. Bioinformatics: is the computational branch of molecular biology Using the computer software to analyze biological data The term in silico biology

3. The course theme Lecture will emphasize the biological concept Lab will use hand on experience to manipulate bioinformatic techniques to analyze this biological concept

4. Course grading system Weekly quizzes: 10 pts each Mid term exam: 50 pts Final exam: 100 pts Oral presentation : 20 points Four internet assignments: 10 pts each Attendance 5 pts / lecture and lab i.e 2.5 pts each /week

5. Structure of DNA

6. Deoxyribonucleic Acid (DNA)  Double-stranded helical molecule found in the nucleus of the cell  Replicates itself before the cell divides, ensuring genetic continuity  Provides instructions for protein synthesis

7. Chemical structure of DNA  Composed of carbon, oxygen, hydrogen, nitrogen, and phosphorus  DNA is a polymer  its structural unit is the nucleotide composed of nitrogenous base composed of nitrogenous base a pentose sugar, a pentose sugar, a phosphate group a phosphate group

8. Chemical structure of DNA Nitrogenous bases

9. Chemical structure of DNA

11. Reading the DNA molecule is from the 5` to 3`

12. Base pairing of DNA  Chargaff's rules:  The amount of adenine equals that of thymine: [A] = [T].  The amount of guanine equals that of cytosine:[G] = [C]  [A] + [G] = [T]+ [C]  The amount of purine base equals that of pyrimidine bases:

13. True or false  The amount of purine base equals that of pyrimidine bases in any DNA molecules

14. DNA is composed of 2 strands  Forward ( 5`-3`)  Reverse ( 3`-5`)  By knowing the sequence of one strand can you deduce the sequence of the other ?

15. How DNA is replicated in living cells?

16. DNA content and the number of genes  DNA content is constant among the same species but it varies among different species  This is Known as C- value

17. C- value paradox  In prokaryotes the number of genes is somehow correlated with the DNA content but this case does not apply to eukaryotes  The DNA size is not correlated with organism complexity

18. Solving the C- value paradox Solving the C- value paradox Why in Eukaryotes the DNA size is not proportional with the number of genes?

19. The C- value and organism complexity Why in Eukaryotes the DNA size is not proportional with the number of genes?

20. The non coding DNA in human  Genomic DNA means the coding and non coding hereditary material  1.5 % of Human DNA codes only for protein  The other 98.5 % are mostly non coding These includes transposable elements

21. The terms  Genome  The hereditary material in an organism  Genomics Comparing the genomes among different species  Genetics Looking at the gene regulation and function

22. Comparative genomics  Computational analysis of different genomes among different organisms  This is to identify - Regulatory sequences - siRNA - Transposable elements - Conserved regions

23. Ultra conserved region in DNA  Indicates functional similarities  Can be used to track down evolutionary events  E.g. The human brain development

24. Ultra conserved region in DNA  DNA regions coding for enzyme binding sites and hormonal receptors are ultra conserved among different organisms

25. DNA molecule in DATABASE  Information about DNA is retrieved from extensively studied model organisms  Model organism criteria: has compact DNA has compact DNA Small genome size with the least amount of junk DNA ( non coding DNA that might include pseudo genes and retro /transposons)

26. DNA molecule in DATABASE Model organism in each species Bacteria ( E. coli and Heamophilus influenza) Fungi ( yeast) Virus ( T4 and Lambda bacteriophage) Worms( Coedorhabditis elegans) Insects ( Drosophylla) Plants ( Arabidopsis) Animals ( rat and mice) Humans ( there is no model but DNA is collected from donor’s blood samples and surgical operations)

27. DNA molecule in DATABASE Identifying the DNA coding region  Open reading frame (ORF)  Regulatory sequences  The coding region is divided into motifs

28. DNA forms  Linear double helix  Circular Relaxed Relaxed Coild Coild Supercoiled Supercoiled

29. The lab session  Different DNA searching engines over the net  Retrieving DNA information by different ways  DNA Data analysis

30.  Thank you  Questions